1
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Gaillard S, Charasson V, Ribeyre C, Salifou K, Pillaire MJ, Hoffmann JS, Constantinou A, Trouche D, Vandromme M. KDM5A and KDM5B histone-demethylases contribute to HU-induced replication stress response and tolerance. Biol Open 2021; 10:268370. [PMID: 34184733 PMCID: PMC8181900 DOI: 10.1242/bio.057729] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/20/2021] [Indexed: 12/25/2022] Open
Abstract
KDM5A and KDM5B histone-demethylases are overexpressed in many cancers and have been involved in drug tolerance. Here, we describe that KDM5A, together with KDM5B, contribute to replication stress (RS) response and tolerance. First, they positively regulate RRM2, the regulatory subunit of ribonucleotide reductase. Second, they are required for optimal levels of activated Chk1, a major player of the intra-S phase checkpoint that protects cells from RS. We also found that KDM5A is enriched at ongoing replication forks and associates with both PCNA and Chk1. Because RRM2 is a major determinant of replication stress tolerance, we developed cells resistant to HU, and show that KDM5A/B proteins are required for both RRM2 overexpression and tolerance to HU. Altogether, our results indicate that KDM5A/B are major players of RS management. They also show that drugs targeting the enzymatic activity of KDM5 proteins may not affect all cancer-related consequences of KDM5A/B overexpression.
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Affiliation(s)
- Solenne Gaillard
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Virginie Charasson
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Cyril Ribeyre
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Kader Salifou
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Marie-Jeanne Pillaire
- Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, University of Toulouse 3, 31037 Toulouse, France
| | - Jean-Sebastien Hoffmann
- Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 avenue Irène-Joliot-Curie, 31059 Toulouse cedex, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Didier Trouche
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Marie Vandromme
- MCD, Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
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2
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Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer. Nat Commun 2021; 12:1628. [PMID: 33712615 PMCID: PMC7955121 DOI: 10.1038/s41467-021-21884-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/22/2021] [Indexed: 01/31/2023] Open
Abstract
Tyrosine kinase inhibitors were found to be clinically effective for treatment of patients with certain subsets of cancers carrying somatic mutations in receptor tyrosine kinases. However, the duration of clinical response is often limited, and patients ultimately develop drug resistance. Here, we use single-cell RNA sequencing to demonstrate the existence of multiple cancer cell subpopulations within cell lines, xenograft tumors and patient tumors. These subpopulations exhibit epigenetic changes and differential therapeutic sensitivity. Recurrently overrepresented ontologies in genes that are differentially expressed between drug tolerant cell populations and drug sensitive cells include epithelial-to-mesenchymal transition, epithelium development, vesicle mediated transport, drug metabolism and cholesterol homeostasis. We show analysis of identified markers using the LINCS database to predict and functionally validate small molecules that target selected drug tolerant cell populations. In combination with EGFR inhibitors, crizotinib inhibits the emergence of a defined subset of EGFR inhibitor-tolerant clones. In this study, we describe the spectrum of changes associated with drug tolerance and inhibition of specific tolerant cell subpopulations with combination agents.
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3
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Halasi M, Hitchinson B, Shah BN, Váraljai R, Khan I, Benevolenskaya EV, Gaponenko V, Arbiser JL, Gartel AL. Honokiol is a FOXM1 antagonist. Cell Death Dis 2018; 9:84. [PMID: 29367668 PMCID: PMC5833612 DOI: 10.1038/s41419-017-0156-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 12/28/2022]
Abstract
Honokiol is a natural product and an emerging drug for a wide variety of malignancies, including hematopoietic malignancies, sarcomas, and common epithelial tumors. The broad range of activity of honokiol against numerous malignancies with diverse genetic backgrounds suggests that honokiol is inhibiting an activity that is common to multiple malignancies. Oncogenic transcription factor FOXM1 is one of the most overexpressed oncoproteins in human cancer. Here we found that honokiol inhibits FOXM1-mediated transcription and FOXM1 protein expression. More importantly, we found that honokiol’s inhibitory effect on FOXM1 is a result of binding of honokiol to FOXM1. This binding is specific to honokiol, a dimerized allylphenol, and was not observed in compounds that either were monomeric allylphenols or un-substituted dihydroxy phenols. This indicates that both substitution and dimerization of allylphenols are required for physical interaction with FOXM1. We thus demonstrate a novel and specific mechanism for FOXM1 inhibition by honokiol, which partially may explain its anticancer activity in cancer cells.
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Affiliation(s)
- Marianna Halasi
- Department of Medicine, University of Illinois, Chicago, IL, USA
| | - Ben Hitchinson
- Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, IL, USA
| | - Binal N Shah
- Department of Medicine, University of Illinois, Chicago, IL, USA
| | - Renáta Váraljai
- Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, IL, USA
| | - Irum Khan
- Department of Medicine, University of Illinois, Chicago, IL, USA
| | | | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, IL, USA
| | - Jack L Arbiser
- Department of Dermatology, Emory University School of Medicine, Atlanta Veterans Administration Medical Center, Atlanta, Georgia, USA
| | - Andrei L Gartel
- Department of Medicine, University of Illinois, Chicago, IL, USA. .,Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, IL, USA.
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4
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Maggi EC, Crabtree JS. Novel targets in the treatment of neuroendocrine tumors: RBP2. INTERNATIONAL JOURNAL OF ENDOCRINE ONCOLOGY 2017. [DOI: 10.2217/ije-2016-0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Retinoblastoma binding protein 2, also known as RBP2, JARID1A or KDM5A, is an H3K4 demethylase implicated in a variety of non-neuroendocrine, and more recently, neuroendocrine tumors (NETs). NETs are tumors that form from neuroendocrine cells in tissues of the GI tract, endocrine pancreas, lung, skin and other tissues. RBP2 is expressed at abnormally high levels in NETs and recent work demonstrates that modulation of RBP2 in vitro and in vivo impacts end points of tumorigenesis. Interestingly, the demethylase activity of RBP2 is not exclusively responsible for these changes, as RBP2's binding partners may mediate its activity in a tissue- or context-dependent manner. Here, we discuss the features of RBP2 and its role in cell cycle regulation, angiogenesis and drug resistance in cancer.
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Affiliation(s)
- Elaine C Maggi
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Judy S Crabtree
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
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5
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Guo T, Ochi T, Nakatsugawa M, Kagoya Y, Anczurowski M, Wang CH, Rahman MA, Saso K, Butler MO, Hirano N. Generating De Novo Antigen-specific Human T Cell Receptors by Retroviral Transduction of Centric Hemichain. J Vis Exp 2016. [PMID: 27805596 DOI: 10.3791/54697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
T cell receptors (TCRs) are used clinically to direct the specificity of T cells to target tumors as a promising modality of immunotherapy. Therefore, cloning TCRs specific for various tumor-associated antigens has been the goal of many studies. To elicit an effective T cell response, the TCR must recognize the target antigen with optimal affinity. However, cloning such TCRs has been a challenge and many available TCRs possess sub-optimal affinity for the cognate antigen. In this protocol, we describe a method of cloning de novo high affinity antigen-specific TCRs using existing TCRs by exploiting hemichain centricity. It is known that for some TCRs, each TCRα or TCRβ hemichain do not contribute equally to antigen recognition, and the dominant hemichain is referred to as the centric hemichain. We have shown that by pairing the centric hemichain with counter-chains differing from the original counter-chain, we are able to maintain the antigen specificity, while modulating its interaction strength for the cognate antigen. Thus, the therapeutic potential of a given TCR can be improved by optimizing the pairing between the centric and counter hemichains.
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Affiliation(s)
- Tingxi Guo
- Department of Immunology, University of Toronto; Princess Margaret Cancer Centre, University Health Network
| | - Toshiki Ochi
- Princess Margaret Cancer Centre, University Health Network
| | | | - Yuki Kagoya
- Princess Margaret Cancer Centre, University Health Network
| | - Mark Anczurowski
- Department of Immunology, University of Toronto; Princess Margaret Cancer Centre, University Health Network
| | - Chung-Hsi Wang
- Department of Immunology, University of Toronto; Princess Margaret Cancer Centre, University Health Network
| | | | - Kayoko Saso
- Princess Margaret Cancer Centre, University Health Network
| | - Marcus O Butler
- Department of Immunology, University of Toronto; Princess Margaret Cancer Centre, University Health Network
| | - Naoto Hirano
- Department of Immunology, University of Toronto; Princess Margaret Cancer Centre, University Health Network;
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6
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Penterling C, Drexler GA, Böhland C, Stamp R, Wilke C, Braselmann H, Caldwell RB, Reindl J, Girst S, Greubel C, Siebenwirth C, Mansour WY, Borgmann K, Dollinger G, Unger K, Friedl AA. Depletion of Histone Demethylase Jarid1A Resulting in Histone Hyperacetylation and Radiation Sensitivity Does Not Affect DNA Double-Strand Break Repair. PLoS One 2016; 11:e0156599. [PMID: 27253695 PMCID: PMC4890786 DOI: 10.1371/journal.pone.0156599] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 05/17/2016] [Indexed: 12/31/2022] Open
Abstract
Histone demethylases have recently gained interest as potential targets in cancer treatment and several histone demethylases have been implicated in the DNA damage response. We investigated the effects of siRNA-mediated depletion of histone demethylase Jarid1A (KDM5A, RBP2), which demethylates transcription activating tri- and dimethylated lysine 4 at histone H3 (H3K4me3/me2), on growth characteristics and cellular response to radiation in several cancer cell lines. In unirradiated cells Jarid1A depletion lead to histone hyperacetylation while not affecting cell growth. In irradiated cells, depletion of Jarid1A significantly increased cellular radiosensitivity. Unexpectedly, the hyperacetylation phenotype did not lead to disturbed accumulation of DNA damage response and repair factors 53BP1, BRCA1, or Rad51 at damage sites, nor did it influence resolution of radiation-induced foci or rejoining of reporter constructs. We conclude that the radiation sensitivity observed following depletion of Jarid1A is not caused by a deficiency in repair of DNA double-strand breaks.
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Affiliation(s)
- Corina Penterling
- Department of Radiation Oncology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Guido A. Drexler
- Department of Radiation Oncology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Claudia Böhland
- Department of Radiation Oncology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Ramona Stamp
- Department of Radiation Oncology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Christina Wilke
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Herbert Braselmann
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Randolph B. Caldwell
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Judith Reindl
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany
| | - Stefanie Girst
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany
| | - Christoph Greubel
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany
| | | | - Wael Y. Mansour
- Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Tumor Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Kerstin Borgmann
- Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Günther Dollinger
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, Neuherberg, Germany
- Clinical Cooperation Group ‘Personalized Radiotherapy of Head and Neck Cancer’, Helmholtz Center Munich, Neuherberg, Germany
| | - Anna A. Friedl
- Department of Radiation Oncology, Ludwig-Maximilians-University of Munich, Munich, Germany
- Clinical Cooperation Group ‘Personalized Radiotherapy of Head and Neck Cancer’, Helmholtz Center Munich, Neuherberg, Germany
- * E-mail:
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7
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Halasi M, Váraljai R, Benevolenskaya E, Gartel AL. A Novel Function of Molecular Chaperone HSP70: SUPPRESSION OF ONCOGENIC FOXM1 AFTER PROTEOTOXIC STRESS. J Biol Chem 2015; 291:142-8. [PMID: 26559972 DOI: 10.1074/jbc.m115.678227] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Indexed: 02/02/2023] Open
Abstract
The oncogenic transcription factor FOXM1 is overexpressed in the majority of human cancers, and it is a potential target for anticancer therapy. We identified proteasome inhibitors as the first type of drugs that target FOXM1 in cancer cells. Here we found that HSP90 inhibitor PF-4942847 and heat shock also suppress FOXM1. The common effector, which was induced after treatment with proteasome and HSP90 inhibitors or heat shock, was the molecular chaperone HSP70. We show that HSP70 binds to FOXM1 following proteotoxic stress and that HSP70 inhibits FOXM1 DNA-binding ability. Inhibition of FOXM1 transcriptional autoregulation by HSP70 leads to the suppression of FOXM1 protein expression. In addition, HSP70 suppression elevates FOXM1 expression, and simultaneous inhibition of FOXM1 and HSP70 increases the sensitivity of human cancer cells to anticancer drug-induced apoptosis. Overall, we determined the unique and novel mechanism of FOXM1 suppression by proteasome inhibitors.
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Affiliation(s)
| | - Renáta Váraljai
- Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60612
| | | | - Andrei L Gartel
- From the Departments of Medicine and Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60612
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8
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Váraljai R, Islam ABMMK, Beshiri ML, Rehman J, Lopez-Bigas N, Benevolenskaya EV. Increased mitochondrial function downstream from KDM5A histone demethylase rescues differentiation in pRB-deficient cells. Genes Dev 2015; 29:1817-34. [PMID: 26314709 PMCID: PMC4573855 DOI: 10.1101/gad.264036.115] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/06/2015] [Indexed: 12/18/2022]
Abstract
The retinoblastoma tumor suppressor protein pRb restricts cell growth through inhibition of cell cycle progression. Increasing evidence suggests that pRb also promotes differentiation, but the mechanisms are poorly understood, and the key question remains as to how differentiation in tumor cells can be enhanced in order to diminish their aggressive potential. Previously, we identified the histone demethylase KDM5A (lysine [K]-specific demethylase 5A), which demethylates histone H3 on Lys4 (H3K4), as a pRB-interacting protein counteracting pRB's role in promoting differentiation. Here we show that loss of Kdm5a restores differentiation through increasing mitochondrial respiration. This metabolic effect is both necessary and sufficient to induce the expression of a network of cell type-specific signaling and structural genes. Importantly, the regulatory functions of pRB in the cell cycle and differentiation are distinct because although restoring differentiation requires intact mitochondrial function, it does not necessitate cell cycle exit. Cells lacking Rb1 exhibit defective mitochondria and decreased oxygen consumption. Kdm5a is a direct repressor of metabolic regulatory genes, thus explaining the compensatory role of Kdm5a deletion in restoring mitochondrial function and differentiation. Significantly, activation of mitochondrial function by the mitochondrial biogenesis regulator Pgc-1α (peroxisome proliferator-activated receptor γ-coactivator 1α; also called PPARGC1A) a coactivator of the Kdm5a target genes, is sufficient to override the differentiation block. Overexpression of Pgc-1α, like KDM5A deletion, inhibits cell growth in RB-negative human cancer cell lines. The rescue of differentiation by loss of KDM5A or by activation of mitochondrial biogenesis reveals the switch to oxidative phosphorylation as an essential step in restoring differentiation and a less aggressive cancer phenotype.
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Affiliation(s)
- Renáta Váraljai
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Abul B M M K Islam
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA; Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Barcelona Biomedical Research Park, Universitat Pompeu Fabra, Barcelona 08003, Spain; Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Michael L Beshiri
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Jalees Rehman
- Section of Cardiology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, USA; Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois 60612, USA
| | - Nuria Lopez-Bigas
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Barcelona Biomedical Research Park, Universitat Pompeu Fabra, Barcelona 08003, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Elizaveta V Benevolenskaya
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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9
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Ambrus AM, Islam ABMMK, Holmes KB, Moon NS, Lopez-Bigas N, Benevolenskaya EV, Frolov MV. Loss of dE2F compromises mitochondrial function. Dev Cell 2014; 27:438-51. [PMID: 24286825 DOI: 10.1016/j.devcel.2013.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 08/06/2013] [Accepted: 10/02/2013] [Indexed: 10/26/2022]
Abstract
E2F/DP transcription factors regulate cell proliferation and apoptosis. Here, we investigated the mechanism of the resistance of Drosophila dDP mutants to irradiation-induced apoptosis. Contrary to the prevailing view, this is not due to an inability to induce the apoptotic transcriptional program, because we show that this program is induced; rather, this is due to a mitochondrial dysfunction of dDP mutants. We attribute this defect to E2F/DP-dependent control of expression of mitochondria-associated genes. Genetic attenuation of several of these E2F/DP targets mimics the dDP mutant mitochondrial phenotype and protects against irradiation-induced apoptosis. Significantly, the role of E2F/DP in the regulation of mitochondrial function is conserved between flies and humans. Thus, our results uncover a role of E2F/DP in the regulation of mitochondrial function and demonstrate that this aspect of E2F regulation is critical for the normal induction of apoptosis in response to irradiation.
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Affiliation(s)
- Aaron M Ambrus
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
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10
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McGee-Lawrence ME, Li X, Bledsoe KL, Wu H, Hawse JR, Subramaniam M, Razidlo DF, Stensgard BA, Stein GS, van Wijnen AJ, Lian JB, Hsu W, Westendorf JJ. Runx2 protein represses Axin2 expression in osteoblasts and is required for craniosynostosis in Axin2-deficient mice. J Biol Chem 2013; 288:5291-302. [PMID: 23300083 DOI: 10.1074/jbc.m112.414995] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Runx2 and Axin2 regulate craniofacial development and skeletal maintenance. Runx2 is essential for calvarial bone development, as Runx2 haploinsufficiency causes cleidocranial dysplasia. In contrast, Axin2-deficient mice develop craniosynostosis because of high β-catenin activity. Axin2 levels are elevated in Runx2(-/-) calvarial cells, and Runx2 represses transcription of Axin2 mRNA, suggesting a direct relationship between these factors in vivo. Here we demonstrate that Runx2 binds several regions of the Axin2 promoter and that Runx2-mediated repression of Axin2 transcription depends on Hdac3. To determine whether Runx2 contributes to the etiology of Axin2 deficiency-induced craniosynostosis, we generated Axin2(-/-):Runx2(+/-) mice. These double mutant mice had longer skulls than Axin2(-/-) mice, indicating that Runx2 haploinsufficiency rescued the craniosynostosis phenotype of Axin2(-/-) mice. Together, these studies identify a key mechanistic pathway for regulating intramembranous bone development within the skull that involves Runx2- and Hdac3-mediated suppression of Axin2 to prevent the untimely closure of the calvarial sutures.
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11
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Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation. Proc Natl Acad Sci U S A 2012; 109:18499-504. [PMID: 23093672 DOI: 10.1073/pnas.1216724109] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Epigenetic regulation underlies the robust changes in gene expression that occur during development. How precisely epigenetic enzymes contribute to development and differentiation processes is largely unclear. Here we show that one of the enzymes that removes the activating epigenetic mark of trimethylated lysine 4 on histone H3, lysine (K)-specific demethylase 5A (KDM5A), reinforces the effects of the retinoblastoma (RB) family of transcriptional repressors on differentiation. Global location analysis showed that KDM5A cooccupies a substantial portion of target genes with the E2F4 transcription factor. During ES cell differentiation, knockout of KDM5A resulted in derepression of multiple genomic loci that are targets of KDM5A, denoting a direct regulatory function. In terminally differentiated cells, common KDM5A and E2F4 gene targets were bound by the pRB-related protein p130, a DREAM complex component. KDM5A was recruited to the transcription start site regions independently of E2F4; however, it cooperated with E2F4 to promote a state of deepened repression at cell cycle genes during differentiation. These findings reveal a critical role of H3K4 demethylation by KDM5A in the transcriptional silencing of genes that are suppressed by RB family members in differentiated cells.
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12
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Seiler DM, Rouquette J, Schmid VJ, Strickfaden H, Ottmann C, Drexler GA, Mazurek B, Greubel C, Hable V, Dollinger G, Cremer T, Friedl AA. Double-strand break-induced transcriptional silencing is associated with loss of tri-methylation at H3K4. Chromosome Res 2011; 19:883-99. [PMID: 21987186 DOI: 10.1007/s10577-011-9244-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/20/2011] [Accepted: 09/16/2011] [Indexed: 01/16/2023]
Abstract
Epigenetic alterations induced by ionizing radiation may contribute to radiation carcinogenesis. To detect relative accumulations or losses of constitutive post-translational histone modifications in chromatin regions surrounding DNA double-strand breaks (DSB), we developed a method based on ion microirradiation and correlation of the signal intensities after immunofluorescence detection of the histone modification in question and the DSB marker γ-H2AX. We observed after ionizing irradiation markers for transcriptional silencing, such as accumulation of H3K27me3 and loss of active RNA polymerase II, at chromatin regions labeled by γ-H2AX. Confocal microscopy of whole nuclei and of ultrathin nuclear sections revealed that the histone modification H3K4me3, which labels transcriptionally active regions, is underrepresented in γ-H2AX foci. While some exclusion of H3K4me3 is already evident at the earliest time amenable to this kind of analysis, the anti-correlation apparently increases with time after irradiation, suggesting an active removal process. Focal accumulation of the H3K4me3 demethylase, JARID1A, was observed at damaged regions inflicted by laser irradiation, suggesting involvement of this enzyme in the DNA damage response. Since no accumulation of the repressive mark H3K9me2 was found at damaged sites, we suggest that DSB-induced transcriptional silencing resembles polycomb-mediated silencing rather than heterochromatic silencing.
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Affiliation(s)
- Doris M Seiler
- Department of Radiation Oncology, University Hospital of Munich, Schillerstr. 42, 80336, Munich, Germany
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